Here are some of the factors that have contributed to the worst rain-related disaster in Japan in over two decades.
Prime Minister Shinzo Abe warned of a "race against time" to rescue flood victims on Sunday, as emergency response teams in the country's western regions search for at least 60 missing, after floods and landslides caused by torrential rains killed over 100 people.
Japanese authorities issued evacuation orders to around five million people during the worst of the rains, but the orders are not mandatory, and many ignored them.
The Fire and Disaster Management Agency estimates that at least 340 homes were totally or partially destroyed, and almost 10,000 homes were flooded.
More than 50 people were unaccounted for as of Tuesday evening, many in the hardest-hit Hiroshima area.
In Kumano, a mountainside community in Hiroshima prefecture that was hit by a landslide last week, Ken Kirioka anxiously watched rescuers toiling through mud, sand and smashed houses to find the missing, including his 76-year-old father, Katsuharu.
In the town of Mihara, roads were transformed into muddy rivers, with dirt piled up on either side as flood water gushed around the wheels of stranded cars.
And with many people stuck in modestly equipped shelters with few possessions, or living in damaged homes with no running water or electricity, the rising temperatures posed a new problem, authorities said.
Several dozen Mihara residents ventured down from shelters on Sunday to inspect the damage to their homes in the Hongo district of the city, where many locals are rice farmers.
The severe rain caused rivers to overflow, in some cases covering whole towns.
Japan Self-Defense Force soldiers rescue people from a flooded area in Mabi town in Kurashiki, Okayama Prefecture, on July 8.
Areas impacted by the flooding in Japan. "We can't get much information about flooded roads, evacuation centre and where to get food", said the 24-year-old, who is still in Okayama.
Some residents of Mabi had shrugged off the warnings given the area's history of floods.
Rescue workers acknowledged the odds of finding people alive were getting longer.
Kyoto, about 300km to the east of Hiroshima, has also been hit by downpours.
"We'll cut through all the bureaucracy to secure the goods people need for their lives, to improve life in the evacuation centers - such as air conditioners as the hot days continue - and then secure temporary housing and the other things people need to rebuild their lives", he said.
Record-breaking rain: Japan's Meteorological Agency said that three hours of rainfall in one area of Kochi prefecture had reached 26.3 centimeters (10.4 inches), so far the highest rain accumulation since 1976, when the organization began measuring rainfall.